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配体-受体+辅因子

df.net
Registered S3 method overwritten by 'cli':
  method     from    
  print.boxx spatstat

cellchat可视化

# pheatmap(mat, display_numbers = FALSE, number_color ="black", cluster_rows = FALSE, 
         # cluster_cols = FALSE, color = colorRampPalette(c("#1E90FF", "white", "#ff2121"))(400), border_color = NA)
table(cor@idents)

       EC1      SMC_3    Mod_SMC Macrophage    T_cell1      SMC_0      SMC_2    T_cell2    T_cell3        EC2 
      4798       1021       1224       9832      12245       3430       1590       4125        366       1294 
    B_cell  Mast_cell      SMC_1 
      2206        430       2294 

mod_SMC – ACKR3

#chord plot
## 免疫细胞 c(4,5,8,9,11) 和SMC c(2,3,6,7,13)的关系
netVisual_chord_gene(cor, sources.use = c(4,5,8,9,11), targets.use = c(2,3,6,7,13), lab.cex = 0.5, legend.pos.y = 30)

##SMC内部
netVisual_chord_gene(cor, sources.use = c(7,13), targets.use = c(2,3,6), lab.cex = 0.5, legend.pos.y = 30)
#指定pathway
pathways.show <- c("TNF") 
# Hierarchy plot
vertex.receiver = c(2,3,6,7,13) # a numeric vector. 
netVisual_aggregate(cor, signaling = pathways.show, layout = "hierarchy", vertex.receiver = vertex.receiver)

netVisual_aggregate(cor, signaling = pathways.show, layout = "circle")

# netVisual_aggregate(cor, signaling = pathways.show, layout = "chord")

# Heatmap
netVisual_heatmap(cor, signaling = pathways.show, color.heatmap = c("#f1f1f1", "#ff2121"))
Do heatmap based on a single object 

#可视化单个配体受体对的影响
netAnalysis_contribution(cor, signaling = pathways.show)

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